Adding to 10X genome.fa and genes.gtf files

Question

[rbronste]

I would like to add some transgenes to the genome.fa and genes.gtf files included with the 10X reference, so that I could stratify the data by these post-clustering. Is there a good way to approach this, in terms of finding the right place in each file for these additions so as not to throw off the cellranger_arc alignment process.

Thanks.

Answer 1

[GenoMax]

See if this helps: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references

[rbronste]

Not sure how I missed this, has the exact answer Im looking for, thanks!